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Calcium in PDB 1m8t: Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form

Enzymatic activity of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form

All present enzymatic activity of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form:
3.1.1.4;

Protein crystallography data

The structure of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form, PDB code: 1m8t was solved by S.Xu, L.Gu, Q.Wang, Y.Shu, Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.99 / 2.10
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 98.060, 98.060, 132.390, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form (pdb code 1m8t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form, PDB code: 1m8t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1m8t

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Calcium binding site 1 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:29.1
occ:1.00
 O A:TYR28 2.2 17.7 1.0
OD2 A:ASP49 2.2 25.5 1.0
O A:HOH1020 2.2 19.9 1.0
O A:GLY30 2.4 23.9 1.0
O A:GLY32 2.4 32.2 1.0
OD1 A:ASP49 2.6 25.6 1.0
O A:HOH1077 2.6 27.7 1.0
CG A:ASP49 2.7 24.9 1.0
C A:TYR28 3.4 17.3 1.0
C A:GLY32 3.5 31.3 1.0
C A:GLY30 3.6 24.6 1.0
N A:GLY30 3.8 21.0 1.0
N A:GLY32 4.0 31.4 1.0
CA A:TYR28 4.1 17.8 1.0
CB A:ASP49 4.2 24.3 1.0
CA A:GLY32 4.2 30.9 1.0
O A:HOH1092 4.3 30.8 1.0
O A:HOH1079 4.3 28.4 1.0
C A:SER31 4.4 31.3 1.0
N A:GLY33 4.4 30.7 1.0
O A:HOH1078 4.4 15.8 1.0
CA A:GLY30 4.4 21.9 1.0
N A:CYS29 4.4 16.8 1.0
C A:CYS29 4.5 19.6 1.0
CA A:GLY33 4.5 32.1 1.0
CB A:TYR28 4.5 17.9 1.0
CA A:CYS29 4.6 18.4 1.0
N A:SER31 4.6 27.4 1.0
O A:HOH1080 4.8 30.7 1.0
O A:HOH1027 4.8 31.3 1.0
CA A:SER31 4.8 30.6 1.0
O A:CYS45 4.8 18.3 1.0
O A:SER31 4.8 31.6 1.0

Calcium binding site 2 out of 6 in 1m8t

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Calcium binding site 2 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:40.7
occ:1.00
 OD1 B:ASP49 2.3 30.3 1.0
O B:GLY32 2.5 42.0 1.0
O B:GLY30 2.5 41.2 1.0
O B:HOH1164 2.6 30.7 1.0
O B:TYR28 2.7 31.9 1.0
O B:HOH1140 2.9 42.1 1.0
CG B:ASP49 3.1 31.8 1.0
OD2 B:ASP49 3.3 33.1 1.0
C B:GLY30 3.6 41.0 1.0
C B:TYR28 3.7 30.0 1.0
C B:GLY32 3.7 42.2 1.0
O B:HOH1016 3.8 22.5 1.0
N B:GLY30 3.8 34.7 1.0
CA B:GLY30 4.2 37.8 1.0
CA B:TYR28 4.3 30.4 1.0
N B:GLY32 4.4 43.7 1.0
CB B:ASP49 4.5 30.2 1.0
CA B:GLY32 4.6 43.2 1.0
C B:CYS29 4.6 32.2 1.0
N B:GLY33 4.7 41.5 1.0
N B:CYS29 4.7 30.1 1.0
C B:SER31 4.7 43.9 1.0
N B:SER31 4.8 42.9 1.0
CB B:TYR28 4.8 30.1 1.0
CA B:GLY33 4.8 40.2 1.0
O B:HOH1068 4.8 15.3 1.0
O B:HOH1133 4.8 33.9 1.0
CA B:CYS29 5.0 30.8 1.0

Calcium binding site 3 out of 6 in 1m8t

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Calcium binding site 3 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1003

b:30.4
occ:1.00
 O C:GLY32 2.2 24.7 1.0
OD2 C:ASP49 2.4 24.4 1.0
OD1 C:ASP49 2.4 23.4 1.0
O C:TYR28 2.6 16.6 1.0
O C:GLY30 2.6 23.4 1.0
CG C:ASP49 2.7 22.6 1.0
O C:HOH1073 2.8 20.5 1.0
C C:GLY32 3.2 24.1 1.0
C C:TYR28 3.7 16.5 1.0
N C:GLY32 3.8 24.8 1.0
C C:GLY30 3.8 22.2 1.0
CA C:GLY32 4.0 23.9 1.0
O C:HOH1074 4.1 8.8 1.0
N C:GLY33 4.2 24.3 1.0
N C:GLY30 4.2 20.9 1.0
CA C:TYR28 4.2 17.1 1.0
CB C:ASP49 4.3 22.2 1.0
C C:SER31 4.3 25.1 1.0
CA C:GLY33 4.4 25.3 1.0
O C:HOH1075 4.6 26.8 1.0
O C:HOH1076 4.7 33.2 1.0
CA C:GLY30 4.7 21.3 1.0
N C:CYS29 4.7 17.5 1.0
CB C:TYR28 4.7 16.3 1.0
N C:SER31 4.8 22.0 1.0
C C:CYS29 4.8 20.3 1.0
CA C:SER31 4.8 23.8 1.0
O C:SER31 4.8 25.9 1.0
CA C:CYS29 4.9 19.3 1.0
O C:CYS45 4.9 16.1 1.0
CD1 C:TYR28 4.9 15.9 1.0

Calcium binding site 4 out of 6 in 1m8t

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Calcium binding site 4 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1004

b:30.9
occ:1.00
 O D:TYR28 2.1 21.6 1.0
O D:GLY30 2.2 27.4 1.0
O D:HOH1025 2.4 22.6 1.0
O D:GLY32 2.5 31.3 1.0
OD2 D:ASP49 2.6 19.8 1.0
OD1 D:ASP49 2.8 22.2 1.0
CG D:ASP49 3.1 21.3 1.0
C D:GLY30 3.3 28.1 1.0
C D:TYR28 3.3 21.7 1.0
N D:GLY30 3.5 24.7 1.0
O1 D:HEZ1009 3.7 42.2 1.0
C D:GLY32 3.7 30.9 1.0
O D:HOH1031 4.0 7.1 1.0
CA D:GLY30 4.0 27.3 1.0
CA D:TYR28 4.1 21.2 1.0
N D:GLY32 4.1 31.1 1.0
C D:SER31 4.2 31.9 1.0
C D:CYS29 4.2 23.2 1.0
N D:CYS29 4.3 22.3 1.0
N D:SER31 4.3 29.8 1.0
CA D:CYS29 4.4 22.8 1.0
CA D:SER31 4.5 31.6 1.0
O D:HOH1092 4.5 27.6 1.0
CA D:GLY32 4.5 30.8 1.0
O D:SER31 4.5 33.9 1.0
CB D:ASP49 4.6 21.2 1.0
CB D:TYR28 4.6 21.4 1.0
N D:GLY33 4.8 30.7 1.0
O D:CYS45 4.8 21.8 1.0
O D:HOH1091 4.8 30.5 1.0
CA D:GLY33 4.9 29.8 1.0

Calcium binding site 5 out of 6 in 1m8t

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Calcium binding site 5 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1005

b:41.2
occ:1.00
 O E:GLY32 2.2 25.8 1.0
OD2 E:ASP49 2.2 26.7 1.0
O E:HOH1036 2.3 23.6 1.0
O E:TYR28 2.3 20.2 1.0
O E:GLY30 2.5 27.4 1.0
OD1 E:ASP49 2.7 27.0 1.0
O E:HOH1103 2.7 17.8 1.0
CG E:ASP49 2.8 27.1 1.0
C E:GLY32 3.2 25.9 1.0
C E:TYR28 3.5 18.3 1.0
C E:GLY30 3.6 27.8 1.0
N E:GLY30 3.8 23.1 1.0
N E:GLY32 3.8 28.8 1.0
O E:HOH1104 3.9 27.3 1.0
CA E:GLY32 4.0 26.3 1.0
CA E:TYR28 4.2 17.8 1.0
N E:GLY33 4.2 26.0 1.0
O E:HOH1031 4.2 36.8 1.0
CB E:ASP49 4.3 25.4 1.0
C E:SER31 4.3 30.1 1.0
CA E:GLY30 4.3 25.9 1.0
CA E:GLY33 4.5 24.9 1.0
N E:CYS29 4.5 19.5 1.0
C E:CYS29 4.6 22.1 1.0
N E:SER31 4.7 29.3 1.0
CB E:TYR28 4.7 17.0 1.0
CA E:CYS29 4.7 21.0 1.0
O E:CYS45 4.8 25.6 1.0
CA E:SER31 4.9 31.0 1.0
O E:SER31 4.9 31.6 1.0
O E:HOH1015 4.9 10.4 1.0

Calcium binding site 6 out of 6 in 1m8t

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Calcium binding site 6 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1006

b:51.1
occ:1.00
 O F:GLY32 1.8 41.9 1.0
O F:GLY30 2.3 36.2 1.0
OD2 F:ASP49 2.5 25.1 1.0
O F:TYR28 2.6 26.4 1.0
OD1 F:ASP49 2.7 25.4 1.0
CG F:ASP49 2.9 24.9 1.0
C F:GLY32 3.0 42.5 1.0
O F:HOH1105 3.1 26.9 1.0
C F:TYR28 3.5 27.0 1.0
C F:GLY30 3.5 36.4 1.0
N F:GLY32 3.7 42.9 1.0
N F:GLY30 3.9 31.1 1.0
CA F:GLY32 3.9 42.7 1.0
N F:GLY33 4.0 43.0 1.0
CA F:TYR28 4.1 28.2 1.0
C F:SER31 4.1 42.3 1.0
CA F:GLY33 4.3 42.3 1.0
O F:HOH1081 4.3 26.4 1.0
CA F:GLY30 4.4 34.1 1.0
CB F:ASP49 4.4 26.7 1.0
N F:CYS29 4.5 27.4 1.0
N F:SER31 4.5 39.0 1.0
CA F:SER31 4.6 41.1 1.0
C F:CYS29 4.6 28.5 1.0
O F:SER31 4.6 42.6 1.0
CB F:TYR28 4.7 29.2 1.0
O F:HOH1035 4.7 11.8 1.0
CA F:CYS29 4.7 27.1 1.0
O F:CYS45 4.9 26.0 1.0

Reference:

S.Xu, L.Gu, Q.Wang, Y.Shu, S.Song, Z.Lin. Structure of A King Cobra Phospholipase A2 Determined From A Hemihedrally Twinned Crystal. Acta Crystallogr.,Sect.D V. 59 1574 2003.
ISSN: ISSN 0907-4449
PubMed: 12925787
DOI: 10.1107/S0907444903014598
Page generated: Mon Jul 7 17:14:23 2025

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